/// <summary>
/// Export to a isolation scheme to a file or to memory.
/// </summary>
/// <param name="fileName">A file on disk to export to, or null to export to memory.</param>
/// <param name="progressMonitor">progress monitor</param>
public void Export(string fileName, IProgressMonitor progressMonitor)
{
if (ExportString == null)
{
StringWriter writer = new StringWriter();
if (HasHeaders)
{
WriteHeaders(writer);
}
if (IsolationScheme.WindowsPerScan.HasValue)
{
WriteMultiplexedWindows(writer, IsolationScheme.WindowsPerScan.Value, progressMonitor);
}
else
{
WriteWindows(writer);
}
ExportString = writer.ToString();
}
if (fileName != null)
{
var saver = new FileSaver(fileName);
if (!saver.CanSave())
{
throw new IOException(string.Format(Resources.AbstractDiaExporter_Export_Cannot_save_to__0__, fileName));
}
var writer = new StreamWriter(saver.SafeName);
writer.Write(ExportString);
writer.Close();
saver.Commit();
}
}
/// <summary>
/// Save the report to a temp file
/// </summary>
/// <returns>The path to the saved temp file.</returns>
private static string GetReportTempPath(ToolMacroInfo toolMacroInfo)
{
SrmDocument doc = toolMacroInfo.Doc;
string reportName = toolMacroInfo.ReportName;
string toolTitle = toolMacroInfo.ToolTitle;
if (String.IsNullOrEmpty(reportName))
{
throw new Exception(string.Format(Resources.ToolMacros_GetReportTempPath_The_selected_tool_0_requires_a_selected_report_Please_select_a_report_for_this_tool_,
toolTitle));
}
var tempFilePath = GetReportTempPath(reportName, toolTitle);
try
{
using (var saver = new FileSaver(tempFilePath))
{
if (!saver.CanSave())
{
throw new IOException();
}
using (var writer = new StreamWriter(saver.SafeName))
{
ToolDescriptionHelpers.GetReport(doc, reportName, toolTitle, toolMacroInfo.ProgressMonitor, writer);
}
saver.Commit();
return(tempFilePath);
}
}
catch (Exception)
{
throw new IOException(Resources.ToolMacros_GetReportTempPath_Error_exporting_the_report__tool_execution_canceled_);
}
}
protected override bool SafeWriteToFile(Control owner, string fileName, Func <Stream, bool> writeFunc)
{
using (var fileSaver = new FileSaver(fileName, true))
{
if (!fileSaver.CanSave(owner))
{
return(false);
}
if (writeFunc(fileSaver.Stream))
{
fileSaver.Commit();
return(true);
}
}
return(false);
}
private void btnExport_Click(object sender, EventArgs e)
{
string strReferenceFile = (string)comboBoxReferenceFile.SelectedItem;
string strSaveFileName = string.Empty;
if (!string.IsNullOrEmpty(_documentFilePath))
{
strSaveFileName = Path.GetFileNameWithoutExtension(_documentFilePath);
}
if (!string.IsNullOrEmpty(strReferenceFile))
{
strSaveFileName += Path.GetFileNameWithoutExtension(strReferenceFile);
}
strSaveFileName += ".ChorusRequest.xml"; // Not L10N
strSaveFileName = strSaveFileName.Replace(' ', '_');
using (var saveFileDialog = new SaveFileDialog {
FileName = strSaveFileName
})
{
if (saveFileDialog.ShowDialog(this) != DialogResult.OK || string.IsNullOrEmpty(saveFileDialog.FileName))
{
return;
}
SpectrumFilter spectrumFilterData = new SpectrumFilter(Document, MsDataFileUri.Parse(strReferenceFile), null);
using (var saver = new FileSaver(saveFileDialog.FileName))
{
if (!saver.CanSave(this))
{
return;
}
using (var stream = new StreamWriter(saver.SafeName))
{
var xmlSerializer = new XmlSerializer(typeof(Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
xmlSerializer.Serialize(stream, spectrumFilterData.ToChromatogramRequestDocument());
}
saver.Commit();
}
}
Close();
}
public void Init()
{
if (_single)
{
if (FileName != null)
{
_saver = new FileSaver(FileName);
if (!_saver.CanSave())
{
throw new IOException(string.Format(Resources.FileIterator_Init_Cannot_save_to__0__, FileName));
}
_writer = new StreamWriter(_saver.SafeName);
}
else
{
StringBuilder sb = new StringBuilder();
MemoryOutput[BaseName] = sb;
_writer = new StringWriter(sb);
}
_writeHeaders(_writer);
}
}
private bool ExportReport(string fileName, char separator)
{
try
{
using (var saver = new FileSaver(fileName))
{
if (!saver.CanSave(this))
{
return(false);
}
using (var writer = new StreamWriter(saver.SafeName))
{
Report report = GetReport();
bool success = false;
using (var longWait = new LongWaitDlg {
Text = Resources.ExportReportDlg_ExportReport_Generating_Report
})
{
longWait.PerformWork(this, 1500, broker =>
{
var status = new ProgressStatus(Resources.ExportReportDlg_GetDatabase_Analyzing_document);
broker.UpdateProgress(status);
Database database = EnsureDatabase(broker, 80, ref status);
if (broker.IsCanceled)
{
return;
}
broker.UpdateProgress(status = status.ChangeMessage(Resources.ExportReportDlg_ExportReport_Building_report));
ResultSet resultSet = report.Execute(database);
if (broker.IsCanceled)
{
return;
}
broker.UpdateProgress(status = status.ChangePercentComplete(95)
.ChangeMessage(Resources.ExportReportDlg_ExportReport_Writing_report));
ResultSet.WriteReportHelper(resultSet, separator, writer, CultureInfo);
writer.Flush();
writer.Close();
if (broker.IsCanceled)
{
return;
}
broker.UpdateProgress(status.Complete());
saver.Commit();
success = true;
});
}
return(success);
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.ExportReportDlg_ExportReport_Failed_exporting_to, fileName, GetExceptionDisplayMessage(x)), x);
return(false);
}
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <Target> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <Target>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedTarget);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Target,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
if (prositDataSourceRadioButton.Checked)
{
// TODO: Need to figure out a better way to do this, use PrositPeptidePrecursorPair?
var doc = _documentUiContainer.DocumentUI;
var peptides = doc.Peptides.ToArray();
var precursorCount = doc.PeptideTransitionGroupCount;
var peptidesPerPrecursor = new PeptideDocNode[precursorCount];
var precursors = new TransitionGroupDocNode[precursorCount];
int index = 0;
for (var i = 0; i < peptides.Length; ++i)
{
var groups = peptides[i].TransitionGroups.ToArray();
Array.Copy(Enumerable.Repeat(peptides[i], groups.Length).ToArray(), 0, peptidesPerPrecursor, index,
groups.Length);
Array.Copy(groups, 0, precursors, index, groups.Length);
index += groups.Length;
}
try
{
PrositUIHelpers.CheckPrositSettings(this, _skylineWindow);
// Still construct the library builder, otherwise a user might configure Prosit
// incorrectly, causing the build to silently fail
Builder = new PrositLibraryBuilder(doc, name, outputPath, () => true, IrtStandard,
peptidesPerPrecursor, precursors, NCE);
}
catch (Exception ex)
{
_helper.ShowTextBoxError(this, ex.Message);
return(false);
}
}
else
{
Builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Id = Helpers.MakeId(textName.Text),
IrtStandard = _driverStandards.SelectedItem,
PreferEmbeddedSpectra = PreferEmbeddedSpectra
};
}
}
return(true);
}
private void ExportLiveReport(string reportName, string reportFile, char reportColSeparator, bool reportInvariant)
{
var viewContext = DocumentGridViewContext.CreateDocumentGridViewContext(_doc, reportInvariant
? DataSchemaLocalizer.INVARIANT
: SkylineDataSchema.GetLocalizedSchemaLocalizer());
var viewInfo = viewContext.GetViewInfo(PersistedViews.MainGroup.Id.ViewName(reportName));
if (null == viewInfo)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__does_not_exist__If_it_has_spaces_in_its_name__use__double_quotes__around_the_entire_list_of_command_parameters_, reportName);
return;
}
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Exporting_report__0____, reportName);
try
{
using (var saver = new FileSaver(reportFile))
{
if (!saver.CanSave())
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__could_not_be_saved_to__1__, reportName, reportFile);
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Check_to_make_sure_it_is_not_read_only_);
}
var status = new ProgressStatus(string.Empty);
IProgressMonitor broker = new CommandProgressMonitor(_out, status);
using (var writer = new StreamWriter(saver.SafeName))
{
viewContext.Export(broker, ref status, viewInfo, writer,
new DsvWriter(reportInvariant ? CultureInfo.InvariantCulture : LocalizationHelper.CurrentCulture, reportColSeparator));
}
broker.UpdateProgress(status.Complete());
saver.Commit();
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Report__0__exported_successfully_to__1__, reportName, reportFile);
}
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__Failure_attempting_to_save__0__report_to__1__, reportName, reportFile);
_out.WriteLine(x.Message);
}
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
string authority = null;
string id = null;
if (libraryBuildAction == LibraryBuildAction.Create)
{
authority = LibraryAuthority;
if (Uri.CheckHostName(authority) != UriHostNameType.Dns)
{
_helper.ShowTextBoxError(textAuthority, Resources.BuildLibraryDlg_ValidateBuilder_The_lab_authority_name__0__is_not_valid_This_should_look_like_an_internet_server_address_e_g_mylab_myu_edu_and_be_unlikely_to_be_used_by_any_other_lab_but_need_not_refer_to_an_actual_server,
authority);
return(false);
}
Settings.Default.LibraryAuthority = authority;
id = textID.Text;
if (!Regex.IsMatch(id, @"\w[0-9A-Za-z_\-]*")) // Not L10N: Easier to keep IDs restricted to these values.
{
_helper.ShowTextBoxError(textID, Resources.BuildLibraryDlg_ValidateBuilder_The_library_identifier__0__is_not_valid_Identifiers_start_with_a_letter_number_or_underscore_and_contain_only_letters_numbers_underscores_and_dashes, id);
return(false);
}
}
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <string> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <string>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedSequence);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Sequence,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
_builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Authority = authority,
Id = id
};
}
return(true);
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
{
return(false);
}
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return(false);
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return(false);
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return(false);
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
{
outputPath += BiblioSpecLiteSpec.EXT;
}
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return(false);
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return(false);
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
return(false);
}
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
if (validateInputFiles)
{
var inputFilesChosen = new List <string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List <Target> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List <Target>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedTarget);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
continue;
}
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Target,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
_builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Id = Helpers.MakeId(textName.Text),
IrtStandard = comboStandards.SelectedItem as IrtStandard
};
}
return(true);
}
private bool ExportReport(string fileName, char separator)
{
try
{
using (var saver = new FileSaver(fileName))
{
if (!saver.CanSave(this))
return false;
using (var writer = new StreamWriter(saver.SafeName))
{
Report report = GetReport();
bool success = false;
using (var longWait = new LongWaitDlg { Text = Resources.ExportReportDlg_ExportReport_Generating_Report })
{
longWait.PerformWork(this, 1500, broker =>
{
var status = new ProgressStatus(Resources.ExportReportDlg_GetDatabase_Analyzing_document);
broker.UpdateProgress(status);
Database database = EnsureDatabase(broker, 80, ref status);
if (broker.IsCanceled)
return;
broker.UpdateProgress(status = status.ChangeMessage(Resources.ExportReportDlg_ExportReport_Building_report));
ResultSet resultSet = report.Execute(database);
if (broker.IsCanceled)
return;
broker.UpdateProgress(status = status.ChangePercentComplete(95)
.ChangeMessage(Resources.ExportReportDlg_ExportReport_Writing_report));
ResultSet.WriteReportHelper(resultSet, separator, writer, CultureInfo);
writer.Flush();
writer.Close();
if (broker.IsCanceled)
return;
broker.UpdateProgress(status.Complete());
saver.Commit();
success = true;
});
}
return success;
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.ExportReportDlg_ExportReport_Failed_exporting_to, fileName, GetExceptionDisplayMessage(x)), x);
return false;
}
}
private void SaveLayout(string fileName)
{
using (var saverUser = new FileSaver(GetViewFile(fileName)))
{
if (saverUser.CanSave())
{
dockPanel.SaveAsXml(saverUser.SafeName);
saverUser.Commit();
}
}
}
private bool ValidateBuilder(bool validateInputFiles)
{
string name;
if (!_helper.ValidateNameTextBox(textName, out name))
return false;
string outputPath = textPath.Text;
if (string.IsNullOrEmpty(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_You_must_specify_an_output_file_path, outputPath);
return false;
}
if (Directory.Exists(outputPath))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_output_path__0__is_a_directory_You_must_specify_a_file_path, outputPath);
return false;
}
string outputDir = Path.GetDirectoryName(outputPath);
if (string.IsNullOrEmpty(outputDir) || !Directory.Exists(outputDir))
{
_helper.ShowTextBoxError(textPath, Resources.BuildLibraryDlg_ValidateBuilder_The_directory__0__does_not_exist, outputDir);
return false;
}
if (!outputPath.EndsWith(BiblioSpecLiteSpec.EXT))
outputPath += BiblioSpecLiteSpec.EXT;
try
{
using (var sfLib = new FileSaver(outputPath))
{
if (!sfLib.CanSave(this))
{
textPath.Focus();
textPath.SelectAll();
return false;
}
}
}
catch (UnauthorizedAccessException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Access_violation_attempting_to_write_to__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return false;
}
catch (IOException)
{
_helper.ShowTextBoxError(textPath, TextUtil.LineSeparate(Resources.BuildLibraryDlg_ValidateBuilder_Failure_attempting_to_create_a_file_in__0__,
Resources.BuildLibraryDlg_ValidateBuilder_Please_check_that_you_have_write_access_to_this_folder_), outputDir);
return false;
}
double cutOffScore;
if (!_helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
return false;
Settings.Default.LibraryResultCutOff = cutOffScore;
var libraryBuildAction = LibraryBuildAction;
string authority = null;
string id = null;
if (libraryBuildAction == LibraryBuildAction.Create)
{
authority = LibraryAuthority;
if (Uri.CheckHostName(authority) != UriHostNameType.Dns)
{
_helper.ShowTextBoxError(textAuthority, Resources.BuildLibraryDlg_ValidateBuilder_The_lab_authority_name__0__is_not_valid_This_should_look_like_an_internet_server_address_e_g_mylab_myu_edu_and_be_unlikely_to_be_used_by_any_other_lab_but_need_not_refer_to_an_actual_server,
authority);
return false;
}
Settings.Default.LibraryAuthority = authority;
id = textID.Text;
if (!Regex.IsMatch(id, @"\w[0-9A-Za-z_\-]*")) // Not L10N: Easier to keep IDs restricted to these values.
{
_helper.ShowTextBoxError(textID, Resources.BuildLibraryDlg_ValidateBuilder_The_library_identifier__0__is_not_valid_Identifiers_start_with_a_letter_number_or_underscore_and_contain_only_letters_numbers_underscores_and_dashes, id);
return false;
}
}
if (validateInputFiles)
{
var inputFilesChosen = new List<string>();
foreach (int i in listInputFiles.CheckedIndices)
{
inputFilesChosen.Add(_inputFileNames[i]);
}
List<string> targetPeptidesChosen = null;
if (cbFilter.Checked)
{
targetPeptidesChosen = new List<string>();
var doc = _documentUiContainer.Document;
foreach (PeptideDocNode nodePep in doc.Peptides)
{
// Add light modified sequences
targetPeptidesChosen.Add(nodePep.ModifiedSequence);
// Add heavy modified sequences
foreach (var nodeGroup in nodePep.TransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
continue;
targetPeptidesChosen.Add(doc.Settings.GetModifiedSequence(nodePep.Peptide.Sequence,
nodeGroup.TransitionGroup.LabelType,
nodePep.ExplicitMods));
}
}
}
_builder = new BiblioSpecLiteBuilder(name, outputPath, inputFilesChosen, targetPeptidesChosen)
{
Action = libraryBuildAction,
IncludeAmbiguousMatches = cbIncludeAmbiguousMatches.Checked,
KeepRedundant = LibraryKeepRedundant,
CutOffScore = cutOffScore,
Authority = authority,
Id = id
};
}
return true;
}
private void btnExport_Click(object sender, EventArgs e)
{
string strReferenceFile = (string) comboBoxReferenceFile.SelectedItem;
string strSaveFileName = string.Empty;
if (!string.IsNullOrEmpty(_documentFilePath))
{
strSaveFileName = Path.GetFileNameWithoutExtension(_documentFilePath);
}
if (!string.IsNullOrEmpty(strReferenceFile))
{
strSaveFileName += Path.GetFileNameWithoutExtension(strReferenceFile);
}
strSaveFileName += ".ChorusRequest.xml"; // Not L10N
strSaveFileName = strSaveFileName.Replace(' ', '_');
using (var saveFileDialog = new SaveFileDialog { FileName = strSaveFileName})
{
if (saveFileDialog.ShowDialog(this) != DialogResult.OK || string.IsNullOrEmpty(saveFileDialog.FileName))
{
return;
}
SpectrumFilter spectrumFilterData = new SpectrumFilter(Document, MsDataFileUri.Parse(strReferenceFile), null);
using (var saver = new FileSaver(saveFileDialog.FileName))
{
if (!saver.CanSave(this))
{
return;
}
using (var stream = new StreamWriter(saver.SafeName))
{
var xmlSerializer = new XmlSerializer(typeof(Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
xmlSerializer.Serialize(stream, spectrumFilterData.ToChromatogramRequestDocument());
}
saver.Commit();
}
}
Close();
}
/// <summary>
/// Export to a isolation scheme to a file or to memory.
/// </summary>
/// <param name="fileName">A file on disk to export to, or null to export to memory.</param>
/// <param name="progressMonitor">progress monitor</param>
public void Export(string fileName, IProgressMonitor progressMonitor)
{
if (ExportString == null)
{
StringWriter writer = new StringWriter();
if (HasHeaders)
WriteHeaders(writer);
if (IsolationScheme.WindowsPerScan.HasValue)
WriteMultiplexedWindows(writer, IsolationScheme.WindowsPerScan.Value, progressMonitor);
else
WriteWindows(writer);
ExportString = writer.ToString();
}
if (fileName != null)
{
var saver = new FileSaver(fileName);
if (!saver.CanSave())
throw new IOException(string.Format(Resources.AbstractDiaExporter_Export_Cannot_save_to__0__, fileName));
var writer = new StreamWriter(saver.SafeName);
writer.Write(ExportString);
writer.Close();
saver.Commit();
}
}
